The Time of Emrys!
by bubbles002
Summary: The Doctor saves Arthur instead of Merlin. But what does destiny have in store for the young warlock? How will everyone react when he regenerates into a...girl? Eventual Fem/Merlin! summary sucks but story is better!
1. Chapter 1: Not cool!

**A/N: Hey guys! I really wanted to do this crossover as I had this idea ages ago but never got it down! Anyways, I hope you like it and as always, please read and review!**

Chapter 1

Merlin stood there, looking at his brother with pleading eyes, but the Doctor was having none of it. "So, you want me to go and save Arthur from getting stabbed by Mordred? Seriously, the things I do for you" said the Doctor. Merlin smiled a little smile. "Thank you Doctor!" he said. He walked out of the TARDIS and didn't look back. He really did owe his brother, big time! But he wouldn't be able to repay him as that was the last time he was ever going to see the doctor. He kept walking until he reached Camlan. Once at Camlan, merlin walked over to the tent that held all the armour and weapons. He didn't expect to find Gwen in there. "What are you doing in here?" asked Gwen. Merlin didn't answer. He grabbed some spare armour and a sword. "No time for questions Gwen, help me into this armour. Now!" was all merlin said? Gwen helped him into his armour and handed him a sword. "Merlin, do you even know how to use a sword?" she asked, still confused as to why merlin needed one. "Yes, but Arthur can't find out that I've been here. Tell him I'm sorry" said Merlin as he left the tent.

Arthur looked at the boy. He was still so young and had his whole life ahead of him, but he chose Morgana over Camelot. "Mordred, think about what you're doing!" he said in a calm tone. "What, like you did when you killed Kara? You don't understand what it's like to live in fear your whole life Arthur! Now, I will make sure you pay for what you have done!" Mordred shouted. Arthur closed his eyes as he waited for the sword to strike him, but it never came. A whizzing sound was coming from behind him. He knew exactly what that sound was. It was the TARDIS.

When he opened his eyes, he was in a room, a big room. He spun round and saw a man with dark brown hair, a brown blazer, black trousers and small boots standing there. The man spun round when he felt Arthur's eyes on him. "Arthur?" said the doctor. "Doctor what's going on?" asked Arthur just a tad confused. The man smiled. "I' don't know but I'm going to find out." he said as he pulled a leaver. The whole room started shaking as it moved. Arthur was holding onto the railings for dear life. The doctor went round to where a brown box was hanging. It looked like a little television screen. His eyes went wide as he looked at it. "NO!" he said. "What's wrong?" asked Arthur as he finally let go of the railing to see what was wrong. On the screen was a picture of merlin and a date underneath it. "That's merlin" Arthur whispered to himself. "Why have you bought this up and what does it mean?" he asked the doctor. "It means a fixed point in time has been created. Merlin has to die at Camlan or Camelot will fall!" said the doctor. He was furious. Merlin was his baby brother and he was going to die.

"Can't you just change time? You said so yourself, you have a TARDIS you can change any part of time that you want" said Arthur. "Not a fixed point I can't. If I do, time won't just stop, it will disintegrate! Merlin has to die or the whole universe will burn" came the reply. Saying that Arthur was shocked would be an understatement. He couldn't just stand there and do nothing. He couldn't let his best friend die. "You told me ages ago that your people, you can change! You can regenerate. If Merlin is your brother, can he do the same?" asked Arthur. The doctor looked at him. "That doesn't matter! If Merlin doesn't die, then we are all doomed!" said The Doctor. Then an idea struck him. "I have an idea" He looked at him oddly. The Doctor just laughed. He was going to use the tesilector to help his brother to cheat death!

**A/N: Hey guy! I know its short but oh well. So what do you think? Like it? Hate it? please let me know!**


	2. Chapter 2: Regeneration!

**A/N: Hey guys! I know a lot of you have been looking forward to this chapter so here it is! I'm so sorry that this was late as I had the 6 weeks holidays and now I'm in year 11 so it's a pretty hectic year! Anyway, on with chapter!**

Chapter 2

Merlin walked across the green and was shocked at all the fallen knights. He knew that Morgana could be brutal, but this, this was just ridiculous! It didn't matter to him now though, as he was going to die anyway. He hated the fact that he would be leaving his brother and all his friends but he couldn't let millions die because he refused to die!

As he walked he saw Morgana and screamed for her. "Morgana!" he shouted. She whirled round and smirked. "Well well, if it isn't the mighty Emrys! Come to accept his death, how sweet." She said cackling. "I know I have to die, but I'll go down fighting!" he said determined. Morgana looked a little shocked at that but picked a sword and they began to fight. Merlin was very skilled with a sword, not that Arthur would ever know nor could he ever. That was one thing you were taught on Galifrey, how to fight with a sword. He thought of Galifrey, he thought of the Doctor and their childhood. He thought of Arthur and Gwen and the knights.

In the end, Merlin lost his footing and Morgana pushed him down to the ground. She smirked evilly at him. "Now Emrys, you will suffer like I did!" she screamed. Merlin closed his eyes and waited for the plunge of the sword. When it finally came, he could feel this fire pumping through his veins. It wasn't his magic this time, it was a new regeneration. He struggled to get up and Morgana looked at him with confusion on her face. Now it was his turn to smirk. "Did I forget to mention that you can't kill me, well, not properly?" he smiled widely as he heard the TARDIS in the background. Out stepped the Doctor and Arthur. He looked at them both in the eyes and whispered "I'm sorry" before he was consumed by a right light.

Once the regeneration was over, Merlin looked at the Doctor and then to Arthur. Arthur was trying hard not to laugh and the doctor and Morgana looked very confused. "What?" he asked confused, the he realised. He was now a she! "I'M A BLODDY GIRL!" he-she said. Everyone, apart from Merlin, burst out laughing.


End file.
